Natural food items and the additional benefits they provide have received considerable attention in recent years. Betalains are nutritious pigments which have valuable biological properties, e.g., antioxidant and free radical scavenging activity. In this study, aqueous betalain extracts were obtained from different coloured cactus pears (purple, red/pink, and orange), amaranth, and beetroot, with and without the addition of ascorbic acid, microwave-heated, and freeze-dried and subsequently analysed by thin layer chromatography (TLC). Beetroot samples without the addition of ascorbic acid (AA) had lower phenols, flavonoids, and ascorbic acid content than beetroot samples extracted with the addition of AA. Amaranth had significantly higher contents of antioxidants than all the other plants. Results for phenolic compounds showed that there were no significant differences between cactus pear cultivars, however, significant differences were seen between the two beetroot samples (microwave-heated with and without AA) as well as amaranth. For flavonoid compounds, amaranth had significantly higher values than all other samples. The lowest flavonoid content was found in beetroot without AA (0.49 mgCE/g). For ascorbic acid, significant differences were noticed between amaranth (71.71 mg/100 g) and samples from cactus pear and beetroot. TLC results showed that purple and red cactus pear samples had the most vivid colours, a reflection of the high betacyanin and betaxanthin contents in the cultivars. Moreover, extracts from cactus pear, beetroot, and amaranth were classified according to a decision tree which was designed by the Code of Federal Regulations/Food Additives Regulation of the EU. The classification of betalain pigment extracts as colouring foods was achieved through enrichment factor calculations and the colourant decision tree. The results showed that the betalain pigment extraction method used is inexpensive, time-saving, energy-saving, non-toxic, and chemical solvent free and yields high concentrations of betalains.